Mercurial > repos > iuc > bcftools_mpileup

comparison bcftools_mpileup.xml @ 4:9a2923126c43 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
author iuc
date Mon, 27 May 2019 14:07:04 -0400
parents 4422d017fe79
children 0bf290bc84ae
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3:4422d017fe79 4:9a2923126c43
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> 3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">mpileup</token> 5 <token name="@EXECUTABLE@">mpileup</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <xml name="bam_flag_options"> 7 <xml name="bam_flag_options">
244 <param label="Quality Options" name="quality_settings" type="select"> 244 <param label="Quality Options" name="quality_settings" type="select">
245 <option value="none" selected="True">defaults</option> 245 <option value="none" selected="True">defaults</option>
246 <option value="adjust">Set base and mapping quality options</option> 246 <option value="adjust">Set base and mapping quality options</option>
247 </param> 247 </param>
248 <when value="adjust"> 248 <when value="adjust">
249 <param name="baq" type="select" optional="true" label="per-Base Alignment Quality"> 249 <param name="baq" type="select" label="per-Base Alignment Quality">
250 <help> 250 <help>
251 --no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments. 251 --no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments.
252 --redo-BAQ; ignore existing BQ tags 252 --redo-BAQ; ignore existing BQ tags
253 </help> 253 </help>
254 <option value="">Default</option>
254 <option value="--no-BAQ">disable BAQ (per-Base Alignment Quality) (no-BAQ)</option> 255 <option value="--no-BAQ">disable BAQ (per-Base Alignment Quality) (no-BAQ)</option>
255 <option value="--redo-BAQ">recalculate BAQ on the fly, ignore existing BQs (redo-BAQ)</option> 256 <option value="--redo-BAQ">recalculate BAQ on the fly, ignore existing BQs (redo-BAQ)</option>
256 </param> 257 </param>
257 <param name="coefficient_for_downgrading" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/> 258 <param name="coefficient_for_downgrading" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/>
258 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/> 259 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/>
342 </assert_contents> 343 </assert_contents>
343 </output> 344 </output>
344 </test> 345 </test>
345 <test> 346 <test>
346 <param name="input_number" value="single" /> 347 <param name="input_number" value="single" />
348 <param name="input_bam" ftype="bam" value="mpileup.1.bam" />
349 <param name="reference_source_selector" value="history" />
350 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
351 <param name="quality_settings" value="adjust" />
352 <param name="output_type" value="v" />
353 <output name="output_file">
354 <assert_contents>
355 <has_text text="mpileup" />
356 <has_text text="HG00100" />
357 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" />
358 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" />
359 </assert_contents>
360 </output>
361 </test>
362 <test>
363 <param name="input_number" value="single" />
347 <param name="input_bam" ftype="cram" value="mpileup.3.cram" /> 364 <param name="input_bam" ftype="cram" value="mpileup.3.cram" />
348 <param name="reference_source_selector" value="history" /> 365 <param name="reference_source_selector" value="history" />
349 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 366 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
350 <param name="output_type" value="v" /> 367 <param name="output_type" value="v" />
351 <output name="output_file"> 368 <output name="output_file">